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Detailed information for vg0206231967:

Variant ID: vg0206231967 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 6231967
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, G: 0.04, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


AGCAGGGCTTCTCTATCAGTGTCTGTGTCATCACTGATTGCTAATGGCAGGGAACTTGAGAAGATGAAGACAGCCAAGAGAGGAATGAGTTTTGGGCAGG[A/G]
AGCAAACAAGCGGATCATTTTGCTGTTGGTGCTGAGGGCAGTGAGGCTTGCTATTTTGCTTATGGCTAATATGTAGGAGGAGGCACGCACTTGCCTTATA

Reverse complement sequence

TATAAGGCAAGTGCGTGCCTCCTCCTACATATTAGCCATAAGCAAAATAGCAAGCCTCACTGCCCTCAGCACCAACAGCAAAATGATCCGCTTGTTTGCT[T/C]
CCTGCCCAAAACTCATTCCTCTCTTGGCTGTCTTCATCTTCTCAAGTTCCCTGCCATTAGCAATCAGTGATGACACAGACACTGATAGAGAAGCCCTGCT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 44.60% 40.40% 0.13% 14.85% NA
All Indica  2759 62.20% 12.60% 0.14% 25.05% NA
All Japonica  1512 2.20% 97.60% 0.00% 0.26% NA
Aus  269 97.80% 0.70% 0.37% 1.12% NA
Indica I  595 48.70% 2.20% 0.50% 48.57% NA
Indica II  465 49.70% 26.70% 0.22% 23.44% NA
Indica III  913 72.20% 14.20% 0.00% 13.58% NA
Indica Intermediate  786 68.20% 10.30% 0.00% 21.50% NA
Temperate Japonica  767 1.80% 97.70% 0.00% 0.52% NA
Tropical Japonica  504 1.60% 98.40% 0.00% 0.00% NA
Japonica Intermediate  241 4.60% 95.40% 0.00% 0.00% NA
VI/Aromatic  96 58.30% 41.70% 0.00% 0.00% NA
Intermediate  90 44.40% 50.00% 1.11% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0206231967 A -> G LOC_Os02g12010.1 missense_variant ; p.Ser7Pro; MODERATE nonsynonymous_codon ; S7P Average:44.458; most accessible tissue: Callus, score: 92.337 benign 1.394 TOLERATED 0.26
vg0206231967 A -> DEL LOC_Os02g12010.1 N frameshift_variant Average:44.458; most accessible tissue: Callus, score: 92.337 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0206231967 3.39E-07 3.83E-19 mr1170 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0206231967 6.89E-06 2.13E-06 mr1170 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0206231967 NA 1.68E-09 mr1301 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0206231967 NA 3.12E-10 mr1410 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0206231967 NA 5.11E-10 mr1714 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0206231967 NA 1.80E-08 mr1030_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0206231967 1.93E-09 3.86E-16 mr1170_2 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0206231967 6.92E-08 1.06E-08 mr1170_2 Ind_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0206231967 NA 4.29E-07 mr1408_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0206231967 NA 5.30E-06 mr1555_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0206231967 NA 6.49E-08 mr1609_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0206231967 NA 1.76E-08 mr1691_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0206231967 NA 3.55E-07 mr1743_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0206231967 NA 3.95E-07 mr1754_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0206231967 NA 5.07E-06 mr1754_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251